Deregulation of ribosomal protein expression and translation promotes breast cancer metastasis [rna-Seq CTCs 2]

We conducted an in vivo genome-wide CRISPR activation screen to identify genes that accelerate distal metastasis by breast cancer patient-derived circulating tumor cells (CTCs) following direct intravascular inoculation in mice. Regulators of translation and ribosomal proteins were prominent among these, and expression of RPL15, a component of the large ribosome subunit, was sufficient to increase metastatic growth in multiple organs. RPL15 overexpression selectively increases translation of other ribosomal proteins and cell cycle regulators. Unsupervised analysis of single-cell RNA sequencing of freshly-isolated CTCs from breast cancer patients identifies a subset with strong ribosomal and protein translation signatures, correlated with increased proliferative markers, epithelial markers and poor clinical outcome. Thus, ribosome protein expression identifies an aggressive subset of CTCs, whose therapeutic targeting may suppress metastatic progression. The CTC-iChip microfluidic device [PMID: 23552373 ] enables isolation of rare viable circulating tumor cells (CTCs) directly from whole blood specimens of patients with cancer, with RNA quality compatible with single-cell RNA sequencing (RNA-seq). We generated RNA-seq profiles of 195 freshly isolated single candidate CTCs or CTC-clusters from 41 women with metastatic breast cancer. Fifty-four candidate CTCs had fewer than 100,000 uniquely mapped reads and therefore were dropped from further consideration. Of the remaining candidate CTCs, 32 expressed PTPRC at a level higher than 10 reads-per-million, so were deemed potential white blood cells and therefore dropped from further consideration. This resulted in profiles of 109 CTCs or CTC-clusters from 33 patients.